Hi, Indeed that seems to short. So if one has excluded natural processes, the artificial ones remain the only possible ones... Your process does have to include a custom index group, for example... see http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark On Tue, Feb 23, 2016 at 4:56 PM Zheng Ruan <zruan1...@gmail.com> wrote: > Hi Mark, > > Thank you for the suggestions, but I don't think it is because of the PBC > artifacts. I do centered my protein and ligand with "-center -pbc mol" > option. The protein itself looks fine without any breaking. It's just the > ATP that moves out and stays at the outer surface of the protein. I don't > think it's possible in such a short time scale (20ns). > > Best, > Ruan > > On Tue, Feb 23, 2016 at 4:32 AM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > It sounds like you are observing artefacts from > > > > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > > > Mark > > > > On Tue, Feb 23, 2016 at 6:18 AM Zheng Ruan <zruan1...@gmail.com> wrote: > > > > > Hi Gromacs Users, > > > > > > I'm running 20ns MD simulation of a protein kinase with ATP bond. I use > > > amber99sb-ildn force field with parameters of ATP derived from the > > database > > > of Richard Bryce. > > > > > > What surprised me is that the ATP molecules displays a huge flexibility > > and > > > conformational change. First, it slipped out from the starting binding > > > pocket. In addition, the plane of adenine ring and ribose sugar rotate > to > > > about 180 degree after 10ns, making the ATP molecule looks weird. I > never > > > run a MD of a protein with ligand before. Is this something normal? > What > > > are possible causes for this? Maybe I should try some other ATP protein > > > complex to see if the same thing happens? Thank you! > > > > > > Ruan > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.